Hi there,
Haddock3 webserver is still under development, and not in production.
We unfortunately highlight it’s use on our website, but it is mainly for beta-testing.
Thanks for reporting this issue, we will look into it.
In my understanding, we try to generare body-restraints (made to keep chain breaks together), but on a ligand this process is not functional.
I will open an issue.
By the time this is solved, please continue using the HADDOCK2.4 webserver, or use the local version of HADDOCK3, that should be fully functional for your purpose.